Question: Turning GO Terms to GO IDs
0
gravatar for kevluv93
3.7 years ago by
kevluv93150
United States
kevluv93150 wrote:

I recently ran gene enrichment on a transcriptome set using Plant MetGenMap. The outputs gave me a list of GO terms that are enriched and their p-values, but many of the GO terms are redundant (like binding is enriched and nucleotide binding is enriched). I'm planning on plugging this dataset into revigo to condense the redundant terms, but I need a good way to turn a large list of GO terms to GO IDs that doesn't involve me typing each individual term into the AmiGO search bar one at a time. Any thoughts? Thank you!

gene ontology • 1.4k views
ADD COMMENTlink modified 3.7 years ago by Sukhdeep Singh9.7k • written 3.7 years ago by kevluv93150

Do you have examples of go-terms and go-ids? Anyways, you probably want the R package GO.db

ADD REPLYlink written 3.7 years ago by Endre Bakken Stovner880

Wait, is GO.db an R package or a textfile with conversions? I've never used R before, I just type in library(GO.db) and R knows where to get that package?

example GO terms: Nucleotide binding, nucleic acid binding, RNA Binding, DNA Binding

 

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by kevluv93150

GO.db is a package that contains the data you need.

To install: 

source("http://bioconductor.org/biocLite.R")
biocLite("GO.db")

If you have not used R before, this might not be the easiest way.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Endre Bakken Stovner880

If there's a text file available with GO terms to GO IDs, I can just do it in excel. Not ideal, but it'll work. I'm going to have to learn R at some point, but right now I can deal with this.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by kevluv93150
0
gravatar for Sukhdeep Singh
3.7 years ago by
Sukhdeep Singh9.7k
Netherlands
Sukhdeep Singh9.7k wrote:

Try this
Converting Gene Ontology Names To Go Ids

ADD COMMENTlink written 3.7 years ago by Sukhdeep Singh9.7k
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